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Did you run the update.zip or the gscript script?
I just downloaded it and tried it again (the update.zip) and it worked as expected.
You might run it again to get it back in sync...as long as CityID isn't found with .apk, the script will keep trying to put them back.
Have you navigated to /system/app with root explorer or a free file explorer to see if those apps are still named .bak?
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Looks like there is an extra "." On CityID.bak
Rename it to .apk then the script should run fine.
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If using root explore there is a r/w button at the top to make that folder writable.
Or open terminal and type the following (hitting enter after each line)
su
mv /system/app/CityID.bak. /system/app/CityID.apk
That should change it.
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also, after doing a backup with Droid Recovery, where is the backup stored? I like to save a copy of my backups to my pc.
Sorry I missed that question.
It is in
/sdcard/clockworkmod/backups
The file names are the date and time that the backup was made and you will need the whole folder
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